Crystal structure of the Staphylococcus aureus Dihydrodipicolinate synthase-pyruvate complex

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase

Girish, T.S.Sharma, E.Gopal, B.

(2008) FEBS Lett 582: 2923-2930

  • DOI: https://doi.org/10.1016/j.febslet.2008.07.035
  • Primary Citation of Related Structures:  
    3DI0, 3DI1

  • PubMed Abstract: 

    Lysine biosynthesis is crucial for cell-wall formation in bacteria. Enzymes involved in lysine biosynthesis are thus potential targets for anti-microbial therapeutics. Dihydrodipicolinate synthase (DHDPS) catalyzes the first step of this pathway. Unlike its homologues, Staphylococcus aureus DHDPS is a dimer both in solution and in the crystal and is not feedback inhibited by lysine. The crystal structure of S. aureus DHDPS in the free and substrate bound forms provides a structural rationale for its catalytic mechanism. The structure also reveals unique conformational features of the S. aureus enzyme that could be crucial for the design of specific non-competitive inhibitors.

  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrodipicolinate synthase
A, B
295Staphylococcus aureus subsp. aureus COLMutation(s): 0 
Gene Names: DHDPS
Find proteins for Q5HG25 (Staphylococcus aureus (strain COL))
Explore Q5HG25 
Go to UniProtKB:  Q5HG25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5HG25
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.44α = 90
b = 117.44β = 90
c = 182.616γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations